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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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TraceDrawer Resource Report Resource Website 10+ mentions |
TraceDrawer (RRID:SCR_025782) | software resource | Software for evaluating, comparing and presenting real-time interaction data. Used for quantification of kinetics and affinity through curve fitting, with large number of binding models to choose from. Can extract experimental information from measurement, requiring minimal user input. | kinetics, affinity, analysis, evaluating, comparing, presenting, real-time interaction data, | Restricted | SCR_025782 | 2026-09-05 06:35:07 | 18 | |||||||||||
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AtomicJ Resource Report Resource Website 1+ mentions |
AtomicJ (RRID:SCR_026023) | data analysis software, data processing software, image analysis software, software application, software resource | Software application for analysis of force microscopy recordings, including images and force curves. Allows for fast and reliable processing of single force curves and force maps, providing estimation of mechanical properties of sample. | force microscopy recordings, images, force curves, analysis, single force curves processing, force maps processing, | European Union structural funds ; Polish Ministry of Science and Higher Education |
PMID:24985823 | Free, Freely available, | SCR_026023 | 2026-09-05 06:35:11 | 4 | |||||||||
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Seattle Childrens Research Institute Behavioral Phenotyping Core Facility Resource Report Resource Website 1+ mentions |
Seattle Childrens Research Institute Behavioral Phenotyping Core Facility (RRID:SCR_026371) | BPC | access service resource, core facility, service resource | Core dedicated to the protocol driven collection, analysis, and reporting of behavioral data using a blend of classic and innovative assays. Supports neuroscience, psychology, pharmacology, genetics, cancer, and development by providing advanced tools and expertise for the precise measurement and interpretation of behavior. | ABRF, precise measurement, interpretation of behavior, collection, analysis, reporting, behavioral data, |
is listed by: ABRF CoreMarketplace has parent organization: Seattle Childrens Research Institute; Washington; USA |
ABRF_3036 | https://coremarketplace.org/?FacilityID=3036&citation=1 | SCR_026371 | , Seattle Childrens Research Institute Behavioral Phenotyping Core, Behavioral Phenotyping Core | 2026-09-05 06:35:20 | 1 | |||||||
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singleCellTK Resource Report Resource Website 1+ mentions |
singleCellTK (RRID:SCR_026813) | SCTK | software resource, software toolkit | Software R package provides interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. Allows users to integrate tools from various packages at different stages of analysis workflow. | importing, quality control, analysis, visualization, single cell RNA-seq data, | Free, Available for download, Freely available | https://www.camplab.net/sctk/ | SCR_026813 | Single Cell ToolKit | 2026-09-05 06:35:32 | 3 | ||||||||
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University of Connecticut Advanced Light Microscopy Core Facility Resource Report Resource Website 1+ mentions |
University of Connecticut Advanced Light Microscopy Core Facility (RRID:SCR_027547) | access service resource, core facility, service resource | Facility provides training and access to advanced light microscopy systems at an hourly rate. In addition, we are available to consult with and support users at every stage of a project including: experimental design, sample preparation, image acquisition, analysis, and data preparation. | ABRF, advanced light microscopy, microscopy, experimental design, sample preparation, image acquisition, analysis, data preparation, |
is listed by: ABRF CoreMarketplace has parent organization: University of Connecticut; Connecticut; USA |
ABRF_5546 | https://https://coremarketplace.org/?FacilityID=5546&citation=1 | SCR_027547 | , University of Connecticut Advanced Light Microscopy Facility, Advanced Light Microscopy Facility | 2026-09-05 06:35:51 | 2 | ||||||||
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Michigan Technological University Materials Characterization and Fabrication Core Facility Resource Report Resource Website |
Michigan Technological University Materials Characterization and Fabrication Core Facility (RRID:SCR_027872) | access service resource, core facility, service resource | Core facility provides tools for imaging, analysis, environmental testing, and micro/nanofabrication. Offers data, expertise, and hands-on training. From advanced materials to environmental systems, MCFF is the hub where discovery meets precision. | ABRF, imaging, analysis, environmental testing, micro, nano, fabrication |
uses: Asylum Research: MFP-3D-BIO Atomic Force Microscope uses: Thermo Fisher: Apreo 2 FE-SEM Electron Microscope is listed by: ABRF CoreMarketplace has parent organization: Michigan Technological University; Houghton; USA |
Open | ABRF_5732 | https://https://coremarketplace.org/?FacilityID=5732&citation=1 | SCR_027872 | , Materials Characterization and Fabrication Facility(MCFF), Michigan Technological University Materials Characterization and Fabrication Facility(MCFF) | 2026-09-05 06:36:01 | 0 | |||||||
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Cornell University Chemistry MS Core Facility Resource Report Resource Website 1+ mentions |
Cornell University Chemistry MS Core Facility (RRID:SCR_028079) | access service resource, core facility, service resource | Core specializes in the analysis of small organic and organometallic analytes. Provides access to mass spectrometers for all. | ABRF, analysis, organic, organometallic, analytes |
is listed by: ABRF CoreMarketplace has parent organization: Cornell University; New York; USA |
Open | ABRF_5812 | https://https://coremarketplace.org/?FacilityID=5812&citation=1 | SCR_028079 | Cornell University Chemistry MS Facility | 2026-09-05 06:36:06 | 1 | |||||||
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Roswell Park Comprehensive Cancer Center Biostatistics and Statistical Genomics Shared Resource BSGSR Core Facility Resource Report Resource Website |
Roswell Park Comprehensive Cancer Center Biostatistics and Statistical Genomics Shared Resource BSGSR Core Facility (RRID:SCR_028371) | access service resource, core facility, service resource | Core offers services in design, oversight, implementation, analysis, publication, and reporting of scientific studies including articulating study objectives and hypotheses, grant writing, conceiving appropriate cost-effective designs and models for achievement of study objectives, monitoring interim and final analyses, and co-authoring abstracts and manuscripts. | ABRF, services, design, oversight, implementation, analysis, publication, reporting of scientific studies |
is listed by: ABRF CoreMarketplace has parent organization: Roswell Park Comprehensive Cancer Center |
ABRF_5904 | https://https://coremarketplace.org/?FacilityID=5904&citation=1 | SCR_028371 | Biostatistics & Statistical Genomics Shared Resource (BSGSR) | 2026-09-05 06:36:11 | 0 | ||||||||
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Mini Analysis Program Resource Report Resource Website 1000+ mentions |
Mini Analysis Program (RRID:SCR_002184) | Mini Analysis | data analysis software, data processing software, software application, software resource | Software tool that detects peaks of any type, any shape, any direction, and any size for neuroscientists who are studying spontaneous activities. Allows detection of virtually any kind of peaks including spontaneous miniature synaptic currents and potentials, action potential spikes, calcium imaging peaks, amperometric peaks, ECG peaks etc. It includes the complex and multiple peak detection algorithm. Has post-detection analyses including essential plots and statistical parameters. Group Analysis provides specialized and detailed analysis options for action potentials, decay fitting, fEPSP/population spikes, amperometry, etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Synaptosoft Inc., analysis, peak, spontaneous, activity, synaptic, current, potential, spike, calcium, image, amperometric, ECG, plot, statistical, parameter | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000143, SCR_014441 | SCR_002184 | Mini Analysis, MiniAnalysis | 2026-09-05 06:24:45 | 1147 | ||||||||
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BrainVision Analyzer Resource Report Resource Website 100+ mentions |
BrainVision Analyzer (RRID:SCR_002356) | BVA | data analysis software, data processing software, software application, software resource | Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more. | Brain Products GmbH, neurophysiology, manage, data, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brain Products |
Commercially available | nlx_155717 | http://www.nitrc.org/projects/bva | SCR_002356 | BrainVision Analyzer, BrainVision Analyzer 2 | 2026-09-05 06:24:47 | 461 | ||||||
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Blind Source Separation and Independent Component Analysis Resource Report Resource Website |
Blind Source Separation and Independent Component Analysis (RRID:SCR_002812) | ICA/BSS, BSS/ICA, | data analysis software, data processing software, software application, software resource, source code | Blind Source Separation and Independent Component Analysis (ICA) algorithms including: An efficient batch algorithm: JADE and Adaptive algorithms: relative gradient algorithms. Associated papers / documentation are included as well as thoughts on Multi-dimensional independent component analysis. * An efficient batch algorithm: JADE - For off-line ICA, an algorithm has been developed based on the (joint) diagonalization of cumulant matrices. "Good" statistical performance is achieved by involving all the cumulants of order 2 and 4 while a fast optimization is obtained by the device of joint diagonalization. JADE has been successfully applied to the processing of real data sets, such as found in mobile telephony and in airport radar as well as to bio-medical signals (ECG, EEG, multi-electrode neural recordings). The strongest point of JADE for applications of ICA is that it works off-the-shelf (no parameter tuning). They advocate using the code provided as a plug-in replacement for PCA (whenever one is willing to investigate if such a replacement is appropriate). The weakest point of the current implementation is that the number of sources (but not of sensors) is limited in practice (by the available memory) to something like 40 or 50 depending on your computer. The JADE algorithm was originally developed to process complex signals, motivated by applications to digital communications. Another implementation is now available which is tuned to process more efficiently real-valued signals. * Adaptive algorithms: relative gradient algorithms - For adaptive source separation, they have developed a class of equivariant algorithms. This means that their performance is independent of the mixing matrix. They are obtained as stochastic relative gradient algorithms. * Multi-dimensional independent component analysis - Performing ICA on ECG signals with the JADE algorithm, it was realized that an interesting extension of the notion of independent component analysis would be to consider an analysis into linear components that would be "as independent as possible" as in ICA, but would be "livin" in subspaces of dimension greater than 1. This could be called "MICA" for Multi-dimensional Independent Component Analysis. | algorithm, analysis, blind, component, separation, signal, source separation, plugin, ecg, eeg, multi-electrode, neural recording, independent component analysis, equivariant algorithm, equivariant, relative gradient, multi-dimensional, matlab, octave, python, c, joint diagonalization, real-valued signal, complex-valued signal | has parent organization: Telecom ParisTech; Paris; France | Free, Freely available, Available for download | nif-0000-24771 | http://www.tsi.enst.fr/icacentral/index.html | SCR_002812 | ICA / BSS, BSS / ICA, BSS and ICA | 2026-09-05 06:24:54 | 0 | ||||||
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GraphPad Prism Resource Report Resource Website 10000+ mentions Rating or validation data |
GraphPad Prism (RRID:SCR_002798) | data analysis software, data processing software, data visualization software, software application, software resource | Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling. | biostatistics, curve, fitting, nonlinear, regression, graphing, statistical, analysis, biology, pharmacology, physiology |
is listed by: SoftCite has parent organization: GraphPad |
Restricted | rid_000081, SCR_015807 | https://www.graphpad.com/features, https://www.graphpad.com/updates/prism-920-release-notes, http://graphpad-prism.software.informer.com/5.0/, https://www.graphpad.com/guides/prism/7/user-guide/index.htm | SCR_002798 | Prism 9.2.0, Graph Pad Prism 7, Graph Pad Prism, GraphPad Prism, Graph pad Prism 5, GraphPad Prism version 9.2.0, Graphpad Prism software, Graph pad Prism 8, Graph pad Prism, Graphpad Prism | 2026-09-05 06:24:53 | 49648 | |||||||
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Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis Resource Report Resource Website 50+ mentions |
Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (RRID:SCR_002676) | CAMERA | analysis service resource, data analysis service, data or information resource, data repository, organization portal, portal, production service resource, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data. | ecology, energy, environment, gene, analysis, bioinformatics, biological, biology, community, cyberinfrastructure, data, dna, genome, genomics, health care, map, marine, metadata, metagenomic, microbial, microbiology, molecular biology, organism, research, scientific, sequence, sequencing, software, tool, training, viral |
is listed by: OMICtools is related to: VIROME has parent organization: University of California at San Diego; California; USA |
Gordon and Betty Moore Foundation | PMID:21045053 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_011924, OMICS_01476, nif-0000-23292 | SCR_002676 | 2026-09-05 06:24:51 | 83 | ||||||
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NUTMEG Resource Report Resource Website 10+ mentions |
NUTMEG (RRID:SCR_002748) | NUTMEG | 1d time-series analysis software, data analysis software, data processing software, image analysis software, signal processing software, software application, software resource, time-series analysis software | Software MEG/EEG analysis toolbox for reconstructing neural activation and overlaying it onto structural MR images. Toolbox runs under MATLAB in conjunction with SPM2 and can be used with Linux/UNIX, Mac OS X, and Windows platforms. | MEG, EEG, analysis, reconstructing, neural, activation, overlaying, structural, MR, image, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at San Francisco; California; USA |
NIBIB EB022717; NIDCD F31 DC006762; NIDCD R01 DC004855 |
PMID:16012626 | nif-0000-24052 | http://www.nitrc.org/projects/nutmeg, | http://www.radiology.ucsf.edu/research/labs/biomagnetic-imaging/nutmeg | SCR_002748 | Neurodynamic Utility Toolbox for Magnetoencephalography and Electroencephalography | 2026-09-05 06:24:53 | 31 | ||||
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Diffusion MRI of Traumatic Brain Injury Resource Report Resource Website |
Diffusion MRI of Traumatic Brain Injury (RRID:SCR_001637) | Diffusion MRI of TBI | data or information resource, portal, topical portal | Project to define a roadmap for diffusion MR imaging of traumatic brain imaging and design an infrastructure to implement the recommendations and tested to ensure feasibility, disseminate results, and facilitate deployment and adoption. The research roadmap and infrastructure development will concentrate on three areas: 1) standardization of diffusion imaging methodology, 2) trial design and patient selection for acute or chronic therapy, and 3) development of multi-center collaborations and repositories for evaluating whether advanced diffusion imaging does improve decision making and TBI patients' outcomes. # DTI MRI reproducability: One of the major areas of investigation in this project is to study the reproducibility of data acquisition and image analysis algorithms. Understanding reproducibility defines a base level of deviation from which scans can be analyzed with statistical significance. As part of this work they are also developing site qualification criteria with the intention of setting limits on the MR system minimal performance for acceptable use in TBI evaluation. # Infrastructure for image storage, analysis and visualization: There is a continuing need to refine and extend software methods for diffusion MRI data analysis and visualization. Not only to translate tools into clinical practice, but also to encourage continuation of the innovation and development of new tools and techniques. To deliver upon these goals they are designing and implementing a storage and computational infrastructure to provide access to shared datasets and intuitive interfaces for analysis and visualization through a variety of tools. A strong emphasis has been placed on providing secure data sharing and the ability to add community defined common data elements. The infrastructure is built upon a Software-as-a-Service model, in which tools are hosted and managed remotely allowing users access through well-defined interfaces. The final service will also facilitate composition or orchestration of workflows composed of different analysis and processing tasks (for example using LONI or XNAT pipelines) with the ultimate goal of providing automated no-click evaluations of diffusion MRI data. # Tool development: The final aspect of this project aims to facilitate and encourage tool development and contribution. By providing access to open datasets, they will create a platform on which tool developers can compare and improve and their tools. When tools are sufficiently mature they can be exposed in the infrastructure mentioned above and used by researchers and other developers. | diffusion tensor imaging, diffusion mri, standard specification, image repository, analysis, visualization, data sharing, common data element, service resource, data set |
is related to: vIST/e is related to: Camino is related to: DTI and Fibertools Software Package is related to: Diffusion Tensor Imaging ToolKit is related to: ExploreDTI is related to: Connectome Mapping Toolkit is related to: TORTOISE is related to: MITK Diffusion is related to: MRtrix is related to: MIPAV: Medical Image Processing and Visualization is related to: DTI Blog is related to: FSL has parent organization: University of Chicago; Illinois; USA |
Traumatic brain injury | NINDS | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153906 | SCR_001637 | 2026-09-05 06:24:37 | 0 | ||||||
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Connectome Mapping Toolkit Resource Report Resource Website 10+ mentions |
Connectome Mapping Toolkit (RRID:SCR_001644) | Connectome Mapping Toolkit | data management software, data or information resource, data processing software, data set, image analysis software, image processing software, software application, software resource, software toolkit | A Python-based open source toolkit for magnetic resonance connectome mapping, data management, sharing, visualization and analysis. The toolkit includes the connectome mapper (a full DMRI processing pipeline), a new file format for multi modal data and metadata, and a visualization application. | magnetic resonance, connectome, mapping, data management, data sharing, visualization, analysis, connectome mapper, processing pipeline, python, connectomics, multi-modal, network analysis, neuroimaging, neuroinformatics tool, mri, knowledge-base, semantic, technology, mapping, source code |
is related to: Diffusion MRI of Traumatic Brain Injury has parent organization: University of Lausanne; Lausanne; Switzerland has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland is parent organization of: Connectome Viewer |
Swiss National Science Foundation 33CM30-124089 | PMID:21713110 | Free, Available for download, Freely available | nlx_153920 | http://www.cmtk.org/, http://www.connectome.ch/ | SCR_001644 | 2026-09-05 06:24:37 | 10 | |||||
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Diffusion Tensor Imaging ToolKit Resource Report Resource Website 10+ mentions |
Diffusion Tensor Imaging ToolKit (RRID:SCR_001642) | DTI-TK | data processing software, image analysis software, software application, software resource, software toolkit | A spatial normalization and atlas construction toolkit optimized for examining white matter morphometry using DTI data with special care taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings. A 2011 study published in NeuroImage ranks DTI-TK the top-performing tool in its class. Key features include: * open standard-based file IO support: NIfTI format for scalar, vector and tensor image volumes * tool chains for manipulating tensor image volumes: resampling, smoothing, warping, registration & visualization * pipelines for WM morphometry: spatial normalization & atlas construction for population-based studies * built-in cluster-computing support: support for open source Sun Grid Engine (SGE) * Interoperability with other popular DTI tools: AFNI, Camino, FSL & DTIStudio * Interoperability with ITK-SNAP: support multi-modal visualization and segmentation | dti, visualization, segmentation, resampling, smoothing, warping, registration, spatial normalization, atlas construction, analysis, atlas application, intersubject, image-to-template, analyze, nifti-1, macos, linux |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Diffusion MRI of Traumatic Brain Injury is related to: Camino is related to: MRI Studio has parent organization: University of Pennsylvania; Philadelphia; USA has parent organization: SourceForge |
NIBIB 1R03EB009321-01 | Free, Available for download, Freely available | nlx_153914 | http://www.nitrc.org/projects/dtitk | SCR_001642 | 2026-09-05 06:24:37 | 25 | ||||||
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Brainstorm Resource Report Resource Website 500+ mentions |
Brainstorm (RRID:SCR_001761) | Brainstorm | data analysis software, data processing software, data visualization software, software application, software resource | Software as collaborative, open source application dedicated to analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology. User-Friendly Application for MEG/EEG Analysis. | MEG, EEG, data, magnetoencephalography, electroencephalography, visualization, processing, analysis, brain, recording, fNIRS, ECoG, electrophysiology |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: OpenMEEG is related to: Open MEG Archive is related to: MATLAB has parent organization: University of Southern California; Los Angeles; USA |
CNRS ; McGill University ; NIBIB R01 EB000473; NIBIB R01 EB002010; NIBIB R01 EB009048; NIBIB R01 EB026299 |
PMID:21584256 | Free, Available for download, Freely available | nif-0000-10267 | http://www.nitrc.org/projects/bst, https://github.com/brainstorm-tools/brainstorm3 | SCR_001761 | brainstorm3 | 2026-09-05 06:24:38 | 622 | ||||
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SeqMonk Resource Report Resource Website 500+ mentions |
SeqMonk (RRID:SCR_001913) | SeqMonk | software resource | Software tool to visualize and analyse high throughput mapped sequence data. | java, high throughput sequencing, mapped, visualization, analysis |
is listed by: OMICtools has parent organization: Babraham Institute |
Free, Available for download, Freely available | OMICS_01936 | http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ | SCR_001913 | 2026-09-05 06:24:41 | 631 | |||||||
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NeuroMorph Resource Report Resource Website 10+ mentions |
NeuroMorph (RRID:SCR_002091) | NeuroMorph | software resource | A toolset for the morphometric analysis and visualization of 3D models derived from electron microscopy image stacks. It is designed to import, analyze, and visualize mesh models. It has been designed specifically for the morphological analysis of 3D objects derived from serial electron microscopy images of brain tissue, although much of its functionality can be applied to any 3D mesh. These models can be generated by software that allows the images to be segmented so that 3D objects can be built. These objects can be generated by any 3D image segmentation software, such as ilastik or Fiji. The NeuroMorph toolset has been developed as a set of add-ons for Blender, a widely used free and open source 3D modeling software package. | electron microscopic imaging assay, morphometry, analysis, visualization, 3d |
is related to: Blender has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland |
Free | SciRes_000156 | SCR_002091 | NeuroMorph Toolkit | 2026-09-05 06:24:44 | 37 |
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